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Jan 12

ParaFold: Paralleling AlphaFold for Large-Scale Predictions

AlphaFold predicts protein structures from the amino acid sequence at or near experimental resolution, solving the 50-year-old protein folding challenge, leading to progress by transforming large-scale genomics data into protein structures. AlphaFold will also greatly change the scientific research model from low-throughput to high-throughput manner. The AlphaFold framework is a mixture of two types of workloads: MSA construction based on CPUs and model inference on GPUs. The first CPU stage dominates the overall runtime, taking hours for a single protein due to the large database sizes and I/O bottlenecks. However, GPUs in this CPU stage remain idle, resulting in low GPU utilization and restricting the capacity of large-scale structure predictions. Therefore, we proposed ParaFold, an open-source parallel version of AlphaFold for high throughput protein structure predictions. ParaFold separates the CPU and GPU parts to enable large-scale structure predictions. ParaFold also effectively reduces the CPU and GPU runtime with two optimizations without compromising the quality of prediction results: using multi-threaded parallelism on CPUs and using optimized JAX compilation on GPUs. We evaluated ParaFold with three datasets of different size and protein lengths. We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19,704 small proteins in five hours on one NVIDIA DGX-2. Using the JAX compile optimization, ParaFold attained a 13.8X average speedup over AlphaFold. ParaFold offers a rapid and effective approach for high-throughput structure predictions, leveraging the predictive power by running on supercomputers, with shorter time, and at a lower cost. The development of ParaFold will greatly speed up high-throughput studies and render the protein "structure-omics" feasible.

  • 6 authors
·
Nov 11, 2021

Sparse Finetuning for Inference Acceleration of Large Language Models

We consider the problem of accurate sparse finetuning of large language models (LLMs), that is, finetuning pretrained LLMs on specialized tasks, while inducing sparsity in their weights. On the accuracy side, we observe that standard loss-based finetuning may fail to recover accuracy, especially at high sparsities. To address this, we perform a detailed study of distillation-type losses, determining an L2-based distillation approach we term SquareHead which enables accurate recovery even at higher sparsities, across all model types. On the practical efficiency side, we show that sparse LLMs can be executed with speedups by taking advantage of sparsity, for both CPU and GPU runtimes. While the standard approach is to leverage sparsity for computational reduction, we observe that in the case of memory-bound LLMs sparsity can also be leveraged for reducing memory bandwidth. We exhibit end-to-end results showing speedups due to sparsity, while recovering accuracy, on T5 (language translation), Whisper (speech translation), and open GPT-type (MPT for text generation). For MPT text generation, we show for the first time that sparse finetuning can reach 75% sparsity without accuracy drops, provide notable end-to-end speedups for both CPU and GPU inference, and highlight that sparsity is also compatible with quantization approaches. Models and software for reproducing our results are provided in Section 6.

  • 5 authors
·
Oct 10, 2023 1

Code generation and runtime techniques for enabling data-efficient deep learning training on GPUs

As deep learning models scale, their training cost has surged significantly. Due to both hardware advancements and limitations in current software stacks, the need for data efficiency has risen. Data efficiency refers to the effective hiding of data access latency and the avoidance of unnecessary data movements. Major challenges arise from the growing disparity between GPU memory bandwidth and computational throughput, imminent GPU memory capacity limitations, and inefficiencies in the PyTorch software stack, including a lack of device-specific PCIe transfer optimizations and high-level domain-specific abstractions. To effectively mitigate these data inefficiencies for deep learning training, this dissertation analyzes data inefficiency in representative deep training tasks, specifically in graph neural networks (GNNs) and large language models (LLMs). It then proposes novel runtime and code generation techniques to mitigate these challenges and implements these optimizations seamlessly within the PyTorch stack while maintaining strong programmability and interoperability. First, PyTorch-Direct is devised to incorporate the GPU-centric PCIe data transfer paradigm in PyTorch for GNN training. Next, Hector intermediate representation (IR) and its code generator are proposed to introduce domain-specific high-level abstraction and systematically address memory-intensive performance challenges for relational GNNs. Finally, in LLM training, the throughput has been increasingly constrained by GPU memory capacity. To mitigate this, the SSDTrain offloading framework is designed and implemented. Together, these contributions show that code generation and runtime techniques can systematically mitigate the data management bottlenecks in deep learning training, which stem from the data-intensive nature of workloads and the oversimplification inherent in the deep learning training software stack.

  • 1 authors
·
Dec 5, 2024

Dissecting the Runtime Performance of the Training, Fine-tuning, and Inference of Large Language Models

Large Language Models (LLMs) have seen great advance in both academia and industry, and their popularity results in numerous open-source frameworks and techniques in accelerating LLM pre-training, fine-tuning, and inference. Training and deploying LLMs are expensive as it requires considerable computing resources and memory, hence many efficient approaches have been developed for improving system pipelines as well as operators. However, the runtime performance can vary significantly across hardware and software stacks, which makes it difficult to choose the best configuration. In this work, we aim to benchmark the performance from both macro and micro perspectives. First, we benchmark the end-to-end performance of pre-training, fine-tuning, and serving LLMs in different sizes , i.e., 7, 13, and 70 billion parameters (7B, 13B, and 70B) on three 8-GPU platforms with and without individual optimization techniques, including ZeRO, quantization, recomputation, FlashAttention. Then, we dive deeper to provide a detailed runtime analysis of the sub-modules, including computing and communication operators in LLMs. For end users, our benchmark and findings help better understand different optimization techniques, training and inference frameworks, together with hardware platforms in choosing configurations for deploying LLMs. For researchers, our in-depth module-wise analyses discover potential opportunities for future work to further optimize the runtime performance of LLMs.

  • 11 authors
·
Nov 6, 2023

FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning

Scaling Transformers to longer sequence lengths has been a major problem in the last several years, promising to improve performance in language modeling and high-resolution image understanding, as well as to unlock new applications in code, audio, and video generation. The attention layer is the main bottleneck in scaling to longer sequences, as its runtime and memory increase quadratically in the sequence length. FlashAttention exploits the asymmetric GPU memory hierarchy to bring significant memory saving (linear instead of quadratic) and runtime speedup (2-4times compared to optimized baselines), with no approximation. However, FlashAttention is still not nearly as fast as optimized matrix-multiply (GEMM) operations, reaching only 25-40\% of the theoretical maximum FLOPs/s. We observe that the inefficiency is due to suboptimal work partitioning between different thread blocks and warps on the GPU, causing either low-occupancy or unnecessary shared memory reads/writes. We propose FlashAttention-2, with better work partitioning to address these issues. In particular, we (1) tweak the algorithm to reduce the number of non-matmul FLOPs (2) parallelize the attention computation, even for a single head, across different thread blocks to increase occupancy, and (3) within each thread block, distribute the work between warps to reduce communication through shared memory. These yield around 2times speedup compared to FlashAttention, reaching 50-73\% of the theoretical maximum FLOPs/s on A100 and getting close to the efficiency of GEMM operations. We empirically validate that when used end-to-end to train GPT-style models, FlashAttention-2 reaches training speed of up to 225 TFLOPs/s per A100 GPU (72\% model FLOPs utilization).

  • 1 authors
·
Jul 17, 2023

A Parallel Region-Adaptive Differential Privacy Framework for Image Pixelization

The widespread deployment of high-resolution visual sensing systems, coupled with the rise of foundation models, has amplified privacy risks in video-based applications. Differentially private pixelization offers mathematically guaranteed protection for visual data through grid-based noise addition, but challenges remain in preserving task-relevant fidelity, achieving scalability, and enabling efficient real-time deployment. To address this, we propose a novel parallel, region-adaptive pixelization framework that combines the theoretical rigor of differential privacy with practical efficiency. Our method adaptively adjusts grid sizes and noise scales based on regional complexity, leveraging GPU parallelism to achieve significant runtime acceleration compared to the classical baseline. A lightweight storage scheme is introduced by retaining only essential noisy statistics, significantly reducing space overhead. Formal privacy analysis is provided under the Laplace mechanism and parallel composition theorem. Extensive experiments on the PETS, Venice-2, and PPM-100 datasets demonstrate favorable privacy-utility trade-offs and significant runtime/storage reductions. A face re-identification attack experiment on CelebA further confirms the method's effectiveness in preventing identity inference. This validates its suitability for real-time privacy-critical applications such as elderly care, smart home monitoring, driver behavior analysis, and crowd behavior monitoring.

  • 1 authors
·
Nov 6, 2025

CUDA-LLM: LLMs Can Write Efficient CUDA Kernels

Large Language Models (LLMs) have demonstrated strong capabilities in general-purpose code generation. However, generating the code which is deeply hardware-specific, architecture-aware, and performance-critical, especially for massively parallel GPUs, remains a complex challenge. In this work, we explore the use of LLMs for the automated generation and optimization of CUDA programs, with the goal of producing high-performance GPU kernels that fully exploit the underlying hardware. To address this challenge, we propose a novel framework called Feature Search and Reinforcement (FSR). FSR jointly optimizes compilation and functional correctness, as well as the runtime performance, which are validated through extensive and diverse test cases, and measured by actual kernel execution latency on the target GPU, respectively. This approach enables LLMs not only to generate syntactically and semantically correct CUDA code but also to iteratively refine it for efficiency, tailored to the characteristics of the GPU architecture. We evaluate FSR on representative CUDA kernels, covering AI workloads and computational intensive algorithms. Our results show that LLMs augmented with FSR consistently guarantee correctness rates. Meanwhile, the automatically generated kernels can outperform general human-written code by a factor of up to 179times in execution speeds. These findings highlight the potential of combining LLMs with performance reinforcement to automate GPU programming for hardware-specific, architecture-sensitive, and performance-critical applications.

  • 5 authors
·
Jun 10, 2025

QMoE: Practical Sub-1-Bit Compression of Trillion-Parameter Models

Mixture-of-Experts (MoE) architectures offer a general solution to the high inference costs of large language models (LLMs) via sparse routing, bringing faster and more accurate models, at the cost of massive parameter counts. For example, the SwitchTransformer-c2048 model has 1.6 trillion parameters, requiring 3.2TB of accelerator memory to run efficiently, which makes practical deployment challenging and expensive. In this paper, we present a solution to this memory problem, in form of a new compression and execution framework called QMoE. Specifically, QMoE consists of a scalable algorithm which accurately compresses trillion-parameter MoEs to less than 1 bit per parameter, in a custom format co-designed with bespoke GPU decoding kernels to facilitate efficient end-to-end compressed inference, with minor runtime overheads relative to uncompressed execution. Concretely, QMoE can compress the 1.6 trillion parameter SwitchTransformer-c2048 model to less than 160GB (20x compression, 0.8 bits per parameter) at only minor accuracy loss, in less than a day on a single GPU. This enables, for the first time, the execution of a trillion-parameter model on affordable commodity hardware, like a single server with 4x NVIDIA A6000 or 8x NVIDIA 3090 GPUs, at less than 5% runtime overhead relative to ideal uncompressed inference. The source code and compressed models are available at github.com/IST-DASLab/qmoe.

  • 2 authors
·
Oct 25, 2023 3

Enabling Fast 2-bit LLM on GPUs: Memory Alignment and Asynchronous Dequantization

Large language models (LLMs) have demonstrated impressive abilities in various domains while the inference cost is expensive. The state-of-the-art methods use 2-bit quantization for mainstream LLMs. However, challenges still exist: (1) Nonnegligible accuracy loss for 2-bit quantization. Weights are quantized by groups, while the ranges of weights are large in some groups, resulting in large quantization errors and nonnegligible accuracy loss (e.g. >3% for Llama2-7b with 2-bit quantization in GPTQ and Greenbit). (2) Limited accuracy improvement by adding 4-bit weights. Increasing 10% extra average bit more 4-bit weights only leads to <0.5% accuracy improvement on a quantized Llama2-7b. (3) Time-consuming dequantization operations on GPUs. The dequantization operations lead to >50% execution time, hindering the potential of reducing LLM inference cost. To tackle these challenges, we propose the following techniques: (1) We only quantize a small fraction of groups with the larger range using 4-bit with memory alignment consideration on GPUs.(2) We design the asynchronous dequantization on GPUs, leading to up to 3.92X speedup. We conduct extensive experiments on different model sizes. We achieve 2.85-bit for each weight and the end-to-end speedup for Llama2-7b is 1.74X over the original model, and we reduce both runtime cost and hardware cost by up to 2.70X and 2.81X with less GPU requirements.

  • 8 authors
·
Nov 27, 2023